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Attention:
The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.

GATK4 ReferenceBase Annotation Error: String index out of range

We haven't transitioned our pipeline for GATK4, so my first GATK4 (4.0.3.0) command is to apply the ReferenceBase annotation to VCFs that we previously generated.

So the invocation was: ./gatk VariantAnnotator -R /scratch/lym_myl_rsch/mma/Green_index/ucsc_hg19.fa -V "/scratch/lym_myl_rsch/mma/Green/Biovest/output/806696_B/806696_B.UnifiedGenotyper.vcf" -A ReferenceBases -O "/scratch/lym_myl_rsch/mma/Green/Biovest/output/806696_B/806696_B.UnifiedGenotyper.refBases.vcf" where the reference is UCSC version of hg19 and the input VCF is one that comes from GATK3.7.0 UnifiedGenotyper.